scholarly journals Three-dimensional optical trapping and orientation of microparticles for coherent X-ray diffraction imaging

2019 ◽  
Vol 116 (10) ◽  
pp. 4018-4024 ◽  
Author(s):  
Yuan Gao ◽  
Ross Harder ◽  
Stephen H. Southworth ◽  
Jeffrey R. Guest ◽  
Xiaojing Huang ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Optical Trapping ◽  
Three Dimensional ◽  
Bragg Diffraction ◽  
X Ray Diffraction ◽  
Diffractive Imaging ◽  
X Ray ◽  
Diffraction Imaging ◽  
Microscopy Techniques ◽  
Micrometer Scale

Optical trapping has been implemented in many areas of physics and biology as a noncontact sample manipulation technique to study the structure and dynamics of nano- and mesoscale objects. It provides a unique approach for manipulating microscopic objects without inducing undesired changes in structure. Combining optical trapping with hard X-ray microscopy techniques, such as coherent diffraction imaging and crystallography, provides a nonperturbing environment where electronic and structural dynamics of an individual particle in solution can be followed in situ. It was previously shown that optical trapping allows the manipulation of micrometer-sized objects for X-ray fluorescence imaging. However, questions remain over the ability of optical trapping to position objects for X-ray diffraction measurements, which have stringent requirements for angular stability. Our work demonstrates that dynamic holographic optical tweezers are capable of manipulating single micrometer-scale anisotropic particles in a microfluidic environment with the precision and stability required for X-ray Bragg diffraction experiments—thus functioning as an “optical goniometer.” The methodology can be extended to a variety of X-ray experiments and the Bragg coherent diffractive imaging of individual particles in solution, as demonstrated here, will be markedly enhanced with the advent of brighter, coherent X-ray sources.

Three-dimensional X-ray diffraction imaging of process-induced dislocation loops in silicon

2011 ◽  
Vol 44 (3) ◽  
pp. 526-531 ◽  
Author(s):  
David Allen ◽  
Jochen Wittge ◽  
Jennifer Stopford ◽  
Andreas Danilewsky ◽  
Patrick McNally
Keyword(s):  
Semiconductor Industry ◽  
Three Dimensional ◽  
Crystal Defects ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Dislocation Loops ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
Relationship Of

In the semiconductor industry, wafer handling introduces micro-cracks at the wafer edge and the causal relationship of these cracks to wafer breakage is a difficult task. By way of understanding the wafer breakage process, a series of nano-indents were introduced both into 20 × 20 mm (100) wafer pieces and into whole wafers as a means of introducing controlled strain. Visualization of the three-dimensional structure of crystal defects has been demonstrated. The silicon samples were then treated by various thermal anneal processes to initiate the formation of dislocation loops around the indents. This article reports the three-dimensional X-ray diffraction imaging and visualization of the structure of these dislocations. A series of X-ray section topographs of both the indents and the dislocation loops were taken at the ANKA Synchrotron, Karlsruhe, Germany. The topographs were recorded on a CCD system combined with a high-resolution scintillator crystal and were measured by repeated cycles of exposure and sample translation along a direction perpendicular to the beam. The resulting images were then rendered into three dimensions utilizing open-source three-dimensional medical tomography algorithms that show the dislocation loops formed. Furthermore this technique allows for the production of a video (avi) file showing the rotation of the rendered topographs around any defined axis. The software also has the capability of splitting the image along a segmentation line and viewing the internal structure of the strain fields.

NONDESTRUCTIVE THREE-DIMENSIONAL X-RAY DIFFRACTION IMAGING OF NANOSCALE PARTICLES

2008 ◽  
Vol 01 (02) ◽  
pp. 207-220
Author(s):  
ANDREI Y. NIKULIN ◽  
RUBEN A. DILANIAN ◽  
BRIAN M. GABLE ◽  
BURRY C. MUDDLE ◽  
JAMES R. HESTER ◽  
...  
Keyword(s):  
Three Dimensional ◽  
X Ray Diffraction ◽  
Nanoscale Particles ◽  
X Ray ◽  
Diffraction Imaging

Bragg and Fresnel Diffraction Imaging Using Highly Coherent X-Rays

1998 ◽  
Vol 4 (S2) ◽  
pp. 376-377
Author(s):  
P. Cloetens ◽  
J. Baruchel ◽  
J.P. Guigay ◽  
W. Ludwig ◽  
L. Mancini ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Optical Path Length ◽  
Fresnel Diffraction ◽  
Crystal Defects ◽  
Bragg Diffraction ◽  
X Rays ◽  
Transmitted Beam ◽  
X Ray ◽  
Diffraction Imaging ◽  
Phase Variations

X-ray imaging started over a century ago. For several decades its only form was absorption radiography, in which contrast is due to local variations in beam attenuation. About forty years ago, a new form of X-ray imagery, Bragg-diffraction imaging or X-ray topography, developed into practical use. It directly reveals crystal defects in the bulk of large single crystals, and paved the way to microelectronics by leading to the growth of large, practically perfect, crystals. The advent of third-generation synchrotron radiation sources of X-rays such as ESRF and APS is now making possible, through the coherence of the X-ray beams, a novel form of radiography, in which contrast arises from phase variations across the transmitted beam, associated with optical path length differences, through Fresnel diffraction. Phase radiography and its three-dimensional companion, X-ray phase tomography, are providing new information on the mechanics of composites as well as on biological materials.

Incorporating particle symmetry into orientation determination in single-particle imaging

2018 ◽  
Vol 74 (5) ◽  
pp. 512-517
Author(s):  
Miklós Tegze ◽  
Gábor Bortel
Keyword(s):  
Three Dimensional ◽  
Symmetric Case ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Particle Imaging ◽  
Single Particle Imaging ◽  
Orientation Determination

In coherent-diffraction-imaging experiments X-ray diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. If the particle has symmetry, finding the orientation of a pattern can be ambiguous. With some modifications, the correlation-maximization method can find the relative orientations of the diffraction patterns for the case of symmetric particles as well. After convergence, the correlation maps show the symmetry of the particle and can be used to determine the symmetry elements and their orientations. The C factor, slightly modified for the symmetric case, can indicate the consistency of the assembled three-dimensional intensity distribution.

scholarly journals Unveiling the spatial distribution of molecular coherences at conical intersections by covariance X-ray diffraction signals

2021 ◽  
Vol 118 (22) ◽  
pp. e2105046118
Author(s):  
Stefano M. Cavaletto ◽  
Daniel Keefer ◽  
Jérémy R. Rouxel ◽  
Flavia Aleotti ◽  
Francesco Segatta ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Three Dimensional ◽  
Laser Pulses ◽  
Conical Intersection ◽  
Conical Intersections ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Diffraction Imaging ◽  
The Rich

The outcomes and timescales of molecular nonadiabatic dynamics are decisively impacted by the quantum coherences generated at localized molecular regions. In time-resolved X-ray diffraction imaging, these coherences create distinct signatures via inelastic photon scattering, but they are buried under much stronger background elastic features. Here, we exploit the rich dynamical information encoded in the inelastic patterns, which we reveal by frequency-dispersed covariance ultrafast powder X-ray diffraction of stochastic X-ray free-electron laser pulses. This is demonstrated for the photoisomerization of azobenzene involving the passage through a conical intersection, where the nuclear wave packet branches and explores different quantum pathways. Snapshots of the coherence dynamics are obtained at high frequency shifts, not accessible with conventional diffraction measurements. These provide access to the timing and to the confined spatial distribution of the valence electrons directly involved in the conical intersection passage. This study can be extended to full three-dimensional imaging of conical intersections with ultrafast X-ray and electron diffraction.

scholarly journals Three-dimensional coherent X-ray diffraction imaging via deep convolutional neural networks

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Longlong Wu ◽  
Shinjae Yoo ◽  
Ana F. Suzana ◽  
Tadesse A. Assefa ◽  
Jiecheng Diao ◽  
...  
Keyword(s):  
Transfer Learning ◽  
Phase Retrieval ◽  
Three Dimensional ◽  
Current Phase ◽  
X Ray Diffraction ◽  
Deep Convolutional Neural Networks ◽  
X Ray ◽  
Model Combining ◽  
Diffraction Imaging ◽  
Improved Performance

AbstractAs a critical component of coherent X-ray diffraction imaging (CDI), phase retrieval has been extensively applied in X-ray structural science to recover the 3D morphological information inside measured particles. Despite meeting all the oversampling requirements of Sayre and Shannon, current phase retrieval approaches still have trouble achieving a unique inversion of experimental data in the presence of noise. Here, we propose to overcome this limitation by incorporating a 3D Machine Learning (ML) model combining (optional) supervised learning with transfer learning. The trained ML model can rapidly provide an immediate result with high accuracy which could benefit real-time experiments, and the predicted result can be further refined with transfer learning. More significantly, the proposed ML model can be used without any prior training to learn the missing phases of an image based on minimization of an appropriate ‘loss function’ alone. We demonstrate significantly improved performance with experimental Bragg CDI data over traditional iterative phase retrieval algorithms.

scholarly journals Femtosecond X-ray diffraction from two-dimensional protein crystals

IUCrJ ◽  
2014 ◽  
Vol 1 (2) ◽  
pp. 95-100 ◽  
Author(s):  
Matthias Frank ◽  
David B. Carlson ◽  
Mark S. Hunter ◽  
Garth J. Williams ◽  
Marc Messerschmidt ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Bragg Diffraction ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Linac Coherent Light Source ◽  
Diffraction Patterns ◽  
Better Than

X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

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